Testing Controls

How to interface with TCGA https://bioconductor.org/packages/devel/bioc/vignettes/TCGAbiolinks/inst/doc/index.html https://bioconductor.org/packages/release/workflows/vignettes/TCGAWorkflow/inst/doc/TCGAWorkflow.html#Environment

Loading the annotation file:

data("IlluminaHumanMethylationEPICanno.ilm10b4.hg19")
anno <- getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)
load("/Users/adiallo/Desktop/Dartmouth/Christiansen_lab/CF_Project/Methylation/Annotation/EPIC.hg19.manifest.RDATA")
attach(annotation)
manifest <- getManifest(IlluminaHumanMethylationEPICmanifest)

Loading the data and metadata information

targets <- read.csv("/Users/adiallo/Desktop/Thesis/Data_Documents/dm_57_samples.csv")
targets$patient <- paste(targets$Sentrix_ID,targets$Sentrix_Position,sep="_")
rownames(targets) <- targets$patient
targets$SampleID<- targets$patient

targets_expanded <- read.csv("/Users/adiallo/Desktop/Thesis/Data_Documents/data_all.csv")
targets_expanded$patient <- paste(targets$Sentrix_ID,targets$Sentrix_Position,sep="_")
rownames(targets_expanded) <- targets_expanded$patient
targets_expanded$SampleID<- targets_expanded$patient
targets = targets_expanded

idat = "/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/no_match/"
RGset_32 = read.metharray.exp("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/no_match/idats/",recursive = TRUE) 
#RGset_25 = openSesame(idat , func = getBetas) 
RGset_25 = read.metharray.exp("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/no_match/25_samples/",recursive = TRUE) 

Get GTEx data

Betas_GTEx = readRDS("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/GTEx/GTEx_samples.rds")
targets_GTEx <- read.csv("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/GTEx/targets.csv")
targets_GTEx$patient <- targets_GTEx$Filename
rownames(targets_GTEx) <- targets_GTEx$patient
targets_GTEx$SampleID<- targets_GTEx$patient

Get TCGA data

tcga.data <- readRDS("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/TCGA/TCGA_data.rds")
tcga.dnam <- tcga.data[["dnam"]]
tcga.pheno <- tcga.data[["pheno"]]
tcga.cell <- tcga.data[["cell_types"]]
msi_dat<-readRDS("/Users/adiallo/Desktop/Thesis/Data_Documents/All_Data/DNA_Methylation/dm_data/TCGA/msi_tcga.rds")
tcga.cell$COAD_Deconv1#$MSS

tcga.cell$COAD_Deconv2#MASS

tcga_T = t(tcga.dnam)

# MSet_noob_T <- preprocessNoob(tcga.dnam)
# beta_matrix_TCGA<-getBeta(MSet_noob_T)

For obtaining more data

files <- getResults(query.met)
head(files$file_id)

[1] "9d067dc1-0dc1-412e-a647-b9203ca503da" "fc14a20c-7c24-4235-8fad-f802355771bc" "8b09dddb-b19e-4ba7-ad11-c634053f9c23"
[4] "49b26be9-b1f8-4f14-8e78-ac5db2ba0d59" "656ae34a-599c-4c0e-83d0-8a3225996e55" "b933669d-424e-4bc4-92f9-467687c28c73"